Fix exportToSQLite errors caused by old table name and parameter order

R/exportToSQLite.r

@@ -1,83 +1,121 @@
-#' @title Export a CDM (Vocabulary and Event tables) into a SQLite Database.
-#'
-#' @description This function fetches (pruned) table data into R dataframes and writes them to a SQLite DB. (Eunomia support)
-#'
-#' @param connectionDetails  An R object of type\cr\code{connectionDetails} created using the
-#'                                     function \code{createConnectionDetails} in the
-#'                                     \code{DatabaseConnector} package.
-#'
-#' @param cdmSchema  The name of the database schema that contains the CDM.
-#'                   Requires read and write permissions to this database. On SQL
-#'                   Server, this should specifiy both the database and the schema,
-#'                   so for example 'cdm_instance.dbo'.
-#'
-#' @param SQLiteDbName         The name of the SQLite Database File.
-#'
-#'@export
-
-exportToSQLite <-
-  function(connectionDetails,
-           cdmSchema,
-           SQLiteDbName = "cdm.sqlite")
-  {
-    conn      <- DatabaseConnector::connect(connectionDetails)
-    sqliteCD  <-
-      DatabaseConnector::createConnectionDetails(dbms = "sqlite", server = SQLiteDbName)
-    sqliteCon <- DatabaseConnector::connect(sqliteCD)
-
-    eventTable <- c(
-      "care_site",
-      "cdm_source",
-      "cohort",
-      "cohort_attribute",
-      "condition_era",
-      "condition_occurrence",
-      "cost",
-      "death",
-      "device_exposure",
-      "dose_era",
-      "drug_era",
-      "drug_exposure",
-      "fact_relationship",
-      "location",
-      "measurement",
-      "metadata",
-      "note",
-      "note_nlp",
-      "observation",
-      "observation_period",
-      "payer_plan_period",
-      "person",
-      "procedure_occurrence",
-      "provider",
-      "specimen",
-      "visit_detail",
-      "visit_occurrence"
-    )
-
-    vocabTable <- c(
-      "concept",
-      "concept_ancestor",
-      "concept_class",
-      "concept_relationship",
-      "concept_synonym",
-      "domain",
-      "drug_strength",
-      "relationship",
-      "source_to_concept_map",
-      "vocabulary"
-    )
-
-    for (tableName in c(eventTable, vocabTable)) {
-      sqlQuery <-
-        paste0("select * from  ", paste0(cdmSchema, ".", tableName), ";")
-      translatedSql <-
-        SqlRender::translate(renderedSql, targetDialect = connectionDetails$dbms)
-      writeLines(paste0("Fetching: ", tableName))
-      tableData <- DatabaseConnector::querySql(conn, translatedSql)
-      DatabaseConnector::insertTable(sqliteCon, toupper(tableName), tableData)
-    }
-
-    DatabaseConnector::disconnect(conn)
-    DatabaseConnector::disconnect(sqliteCon)
-  }
+#' @title Export a CDM (Vocabulary and Event tables) into a SQLite Database.
+#'
+#' @description This function fetches (pruned) table data into R dataframes and writes them to a SQLite DB. (Eunomia support)
+#'
+#' @param connectionDetails  An R object of type\cr\code{connectionDetails} created using the
+#'                                     function \code{createConnectionDetails} in the
+#'                                     \code{DatabaseConnector} package.
+#'
+#' @param cdmSchema  The name of the database schema that contains the CDM.
+#'                   Requires read and write permissions to this database. On SQL
+#'                   Server, this should specifiy both the database and the schema,
+#'                   so for example 'cdm_instance.dbo'.
+#'
+#' @param SQLiteDbName         The name of the SQLite Database File.
+#'
+#'@export
+
+exportToSQLite <-
+  function(connectionDetails,
+           cdmSchema,
+           cdmVersion,
+           SQLiteDbName = "cdm.sqlite")
+  {
+    conn      <- DatabaseConnector::connect(connectionDetails)
+    sqliteCD  <-
+      DatabaseConnector::createConnectionDetails(dbms = "sqlite", server = SQLiteDbName)
+    sqliteCon <- DatabaseConnector::connect(sqliteCD)
+
+    if (cdmVersion == "5.3")
+      eventTable <- c(
+        "attribute_definition",
+        "care_site",
+        "cdm_source",
+        "cohort_definition",
+        "condition_era",
+        "condition_occurrence",
+        "cost",
+        "death",
+        "device_exposure",
+        "dose_era",
+        "drug_era",
+        "drug_exposure",
+        "fact_relationship",
+        "location",
+        "measurement",
+        "metadata",
+        "note",
+        "note_nlp",
+        "observation",
+        "observation_period",
+        "payer_plan_period",
+        "person",
+        "procedure_occurrence",
+        "provider",
+        "specimen",
+        "visit_detail",
+        "visit_occurrence"
+      )
+    else if (cdmVersion == "5.4")
+      eventTable <- c(
+        "care_site",
+        "cdm_source",
+        "cohort",
+        "cohort_definition",
+        "condition_era",
+        "condition_occurrence",
+        "cost",
+        "death",
+        "device_exposure",
+        "dose_era",
+        "drug_era",
+        "drug_exposure",
+        "episode",
+        "episode_event",
+        "fact_relationship",
+        "location",
+        "measurement",
+        "metadata",
+        "note",
+        "note_nlp",
+        "observation",
+        "observation_period",
+        "payer_plan_period",
+        "person",
+        "procedure_occurrence",
+        "provider",
+        "specimen",
+        "visit_detail",
+        "visit_occurrence"
+      )
+    else
+      stop("Unsupported CDM specified. Supported CDM versions are \"5.3\" and \"5.4\"")
+
+
+
+    vocabTable <- c(
+      "concept",
+      "concept_ancestor",
+      "concept_class",
+      "concept_relationship",
+      "concept_synonym",
+      "domain",
+      "drug_strength",
+      "relationship",
+      "source_to_concept_map",
+      "vocabulary"
+    )
+
+    for (tableName in c(eventTable, vocabTable)) {
+      sqlQuery <-
+        paste0("select * from  ", paste0(cdmSchema, ".", tableName), ";")
+      translatedSql <-
+        SqlRender::translate(sql=sqlQuery, targetDialect = connectionDetails$dbms)
+      writeLines(paste0("Fetching: ", tableName))
+      tableData <- DatabaseConnector::querySql(connection=conn, sql=translatedSql)
+      DatabaseConnector::insertTable(connection=sqliteCon, tableName=toupper(tableName), data=tableData)
+    }
+
+    DatabaseConnector::disconnect(conn)
+    DatabaseConnector::disconnect(sqliteCon)
+  }